Sigma-2 (sigma(2)) binding sites are an emerging target for anti-neoplastic agents due to the strong apoptotic effect exhibited by sigma(2) agonists in vitro and the overexpression of these sites in tumor cells. Nonetheless, no sigma(2) receptor protein has been identified. Affinity chromatography using the high-affinity sigma(2) ligand PB28 and human SK-N-SH neuroblastoma cells was previously utilized to identify sigma(2) ligand binding proteins, specifically histones H1, H2A, H2B, and H3.3a. To rationalize this finding, homology modeling and automated docking studies were employed to probe intermolecular interactions between PB28 and human nucleosomal proteins. These studies predicted interaction of PB28 with the H2A/H2B dimer at a series of sites previously found to be implicated in chromatin compaction and nucleosomal assembly. To experimentally verify this prediction, a competitive binding assay was performed on the reconstituted H2A/H2B dimer using [(3)H]PB28 as radioligand, and an IC(50) value of 0.50 nM was determined for PB28 binding. In addition, [(3)H]PB28 was found to accumulate with up to a fivefold excess in nuclear fractions over cytosolic fractions of SK-N-SH and MCF7 cells, indicating that PB28 is capable of entering the nucleus to interact with histone proteins. In conjunction with computational results, these data suggest that PB28 may exert its cytotoxic effect through direct interaction with nuclear material.